RNA-dependent chromatin localization of KDM4D lysine demethylase promotes H3K9me3 demethylation

Abstract

The JmjC-containing lysine demethylase, KDM4D, demethylates di-and tri-methylation of histone H3 on lysine 9 (H3K9me3). How KDM4D is recruited to chromatin and recognizes its histone substrates remains unknown. Here, we show that KDM4D binds RNA independently of its demethylase activity. We mapped two non-canonical RNA binding domains: the first is within the N-terminal spanning amino acids 115 to 236, and the second is within the C-terminal spanning amino acids 348 to 523 of KDM4D. We also demonstrate that RNA interactions with KDM4D N-terminal region are critical for its association with chromatin and subsequently for demethylating H3K9me3 in cells. This study implicates, for the first time, RNA molecules in regulating the levels of H3K9 methylation by affecting KDM4D association with chromatin.

Lysine-Specific Histone Demethylases Contribute to Cellular Differentiation and Carcinogenesis

“…Interestingly, it was recently reported that KDM4D is able to bind RNA through two distinct RNA-binding domains, one of which is the JmjC domain. The KDM4D binding to RNA is independent of KDM4D demethylase activity and is required for its association with chromatin [91]. Whether all the JmjC-containing proteins require RNA for their enzymatic activity as well as for their association with chromatin is still unknown and should be clarified by further studies.…”

The emerging role of lysine demethylases in DNA damage response: dissecting the recruitment mode of KDM4D/JMJD2D to DNA damage sites

“…Toward this end, we took advantage of KDM4D-1H4R-HRK mutant that lost its ability to bind RNA molecules and shows defective chromatin localization. 62 Laser microirradiation assay, performed on U2OS cells expressing EGFP-KDM4D-1H4R-HRK mutant, shows no detectable accumulation of the mutant at DNA breakage sites (Fig. 3).…”

“…One possible explanation for these apparently contradictory results is that the defective accumulation of KDM4D-1H4R-HRK at DNA damage sites results from the fact that KDM4D-1H4R-HRK is found in the nuclear soluble fraction but not in the chromatinbound fraction. 62 In other words, 1H4R-HRK mutations exhibit dominant negative effect and suppress the ability of the C-terminal region to recruit KDM4D to damage sites.…”

“…Additionally, we generated KDM4D mutant that lost its ability to bind RNA and demonstrated that KDM4D-RNA interactions are critical for KDM4D association with chromatin and subsequently for H3K9me3 demethylation in vivo. 62 Additionally, we have previously described a novel function of KDM4D in DDR. We found that KDM4D lysine demethylase is transiently recruited to DNA damage sites in a PARP1-dependent manner.…”

KDM4D crosstalks with PARP1 and RNA at DNA DSBs

“…Mutating His115/ 219, Arg222/225/228/236/123 and Lys127 of KDM4D results in loss of RNA and chromatin binding. 7 This mutant, which can no longer bind RNA, failed to accumulate at DNA damage sites, indicating that KDM4D-RNA interaction is required for its DNA damage accumulation. 6 Altogether, these studies implicate PARP1 and yet unidentified RNA molecules in regulating KDM4D function in the DDR.…”